Correct spelling errors across entire source

Author: prckent

CMake/ClangCompilers.cmake

@@ -14,7 +14,7 @@ IF(QMC_OMP)
   SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
 ENDIF(QMC_OMP)
 
-# Set clang specfic flags (which we always want)
+# Set clang specific flags (which we always want)
 ADD_DEFINITIONS( -Drestrict=__restrict__ )
 
 SET(CMAKE_C_FLAGS     "${CMAKE_C_FLAGS} -fomit-frame-pointer -fstrict-aliasing")

CMake/FindMKL.cmake

@@ -1,9 +1,9 @@
-# Simple file to find MKL (if availible)
+# Simple file to find MKL (if available)
 # This needs a lot of work to make it robust
 INCLUDE( CheckCXXSourceCompiles )
 
 # Extremely Basic Support of common mkl module environment variables
-# or -DMKLROOT/-DMKL_HOME instead of prefered -DMKL_ROOT
+# or -DMKLROOT/-DMKL_HOME instead of preferred -DMKL_ROOT
 if (NOT MKL_ROOT)
   find_path(MKL_ROOT "mkl.h"
     HINTS ${MKLROOT} ${MKL_HOME} $ENV{MKLROOT} $ENV{MKL_ROOT} $ENV{MKL_HOME}

CMake/GNUCompilers.cmake

@@ -13,7 +13,7 @@ IF(QMC_OMP)
   SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
 ENDIF(QMC_OMP)
 
-# Set gnu specfic flags (which we always want)
+# Set gnu specific flags (which we always want)
 ADD_DEFINITIONS( -Drestrict=__restrict__ )
 
 SET(CMAKE_C_FLAGS     "${CMAKE_C_FLAGS} -fomit-frame-pointer -finline-limit=1000 -fstrict-aliasing -funroll-all-loops")

CMake/ctest_script.cmake

@@ -2,8 +2,8 @@
 # Usage:  ctest -s script,build
 #   build = debug / optimized / valgrind / coverage
 # Note: this test will use use the number of processors defined in the variable N_PROCS,
-#   the enviornmental variables
-#   N_PROCS, or the number of processors availible (if not specified)
+#   the environmental variables
+#   N_PROCS, or the number of processors available (if not specified)
 #   N_PROCS_BUILD, or N_PROCS (if not specified)
 #   N_CONCURRENT_TESTS, or N_PROCS (if not specified)
 #   TEST_SITE_NAME, or HOSTNAME (if not specified)

CMakeLists.txt

@@ -179,11 +179,11 @@ SET(BUILD_UNIT_TESTS 1 CACHE BOOL "Build unit tests")
 SET(BUILD_SANDBOX 1 CACHE BOOL "Build sandbox tests and miniapps")
 SET(BUILD_LMYENGINE_INTERFACE 1 CACHE BOOL "Build LMY engine")
 IF (QMC_CUDA AND BUILD_LMYENGINE_INTERFACE)
-  MESSAGE(STATUS "LMY engine is not compatiable with CUDA build! Disabling LMY engine")
+  MESSAGE(STATUS "LMY engine is not compatible with CUDA build! Disabling LMY engine")
   SET(BUILD_LMYENGINE_INTERFACE 0)
 ENDIF()
 IF(MIXED_PRECISION AND BUILD_LMYENGINE_INTERFACE)
-  MESSAGE(STATUS "LMY engine is not compatiable with CPU mixed precision build! Disabling LMY engine")
+  MESSAGE(STATUS "LMY engine is not compatible with CPU mixed precision build! Disabling LMY engine")
   SET(BUILD_LMYENGINE_INTERFACE 0)
 ENDIF()
 SET(BUILD_AFQMC 0 CACHE BOOL "Build with AFQMC")

README.md

@@ -65,9 +65,9 @@ make -j 8
 
 ## Set the environment
 
- A number of enviornmental variables affect the build.  In particular
+ A number of environmental variables affect the build.  In particular
  they can control the default paths for libraries, the default
- compilers, etc.  The list of enviornmental variables is given below:
+ compilers, etc.  The list of environmental variables is given below:
 
 | Environment variable | Description |
 |----------------------|-------------|
@@ -81,10 +81,10 @@ make -j 8
 
 ## CMake options
 
- In addition to reading the enviornmental variables, CMake provides a
+ In addition to reading the environmental variables, CMake provides a
  number of optional variables that can be set to control the build and
  configure steps.  When passed to CMake, these variables will take
- precident over the enviornmental and default variables.  To set them
+ precident over the environmental and default variables.  To set them
  add -D FLAG=VALUE to the configure line between the cmake command and
  the path to the source directory.
 

doxygen/Doxyfile

@@ -1832,7 +1832,7 @@ UML_LOOK               = NO
 # the class node. If there are many fields or methods and many nodes the
 # graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
 # threshold limits the number of items for each type to make the size more
-# managable. Set this to 0 for no limit. Note that the threshold may be
+# manageable. Set this to 0 for no limit. Note that the threshold may be
 # exceeded by 50% before the limit is enforced.
 
 UML_LIMIT_NUM_FIELDS   = 10

doxygen/Doxyfile.ug

@@ -1747,7 +1747,7 @@ UML_LOOK               = NO
 # the class node. If there are many fields or methods and many nodes the
 # graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
 # threshold limits the number of items for each type to make the size more
-# managable. Set this to 0 for no limit. Note that the threshold may be
+# manageable. Set this to 0 for no limit. Note that the threshold may be
 # exceeded by 50% before the limit is enforced.
 
 UML_LIMIT_NUM_FIELDS   = 10

doxygen/OrbitalOptimization.tex

@@ -11,7 +11,7 @@
 \newcommand{\Aopt}{\tilde{A}}
 
 \section{Trial wave functions in logarithmic form}
-Let us consider a trial wave funciton, $\psi$, which is a product of
+Let us consider a trial wave function, $\psi$, which is a product of
 components,
 \begin{equation}
   \psi = \psi_1 \psi_2 \psi_3 \dots

doxygen/dev/basic.dox

@@ -66,7 +66,7 @@ Simply add new files to the INPUT list in \c ug.cfg or \c dev.cfg and run \c dox
 \code
 INPUT =  ug/index.dox ug/gettingstarted.dox ug/somethingnew.dox
 \endcode
-See an exmaple <tt>ug/qmc.dox</tt>. 
+See an example <tt>ug/qmc.dox</tt>. 
 
 <!--
 Each page has

doxygen/dev/index.dox

@@ -7,7 +7,7 @@ The most recent released version is available at
 https://www.qmcpack.org under UIUC/NCSA open-source licence. Those who
 are interested in QMCPACK development are strongly encouraged to
 contact the developers to establish collaborations so that one can
-access to the developers' svn respository. This is exactly the same as
+access to the developers' svn repository. This is exactly the same as
 the release version except for being (i) slightly more recent, (ii) having fewer bugs due to bugfixes, and (iii) potentially having new bugs due to new features.
 Although it is not required, the developers will appreciate if any new
 software can be made available to others when the research and development

doxygen/qmcpack.cfg

@@ -1610,7 +1610,7 @@ UML_LOOK               = NO
 # the class node. If there are many fields or methods and many nodes the
 # graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
 # threshold limits the number of items for each type to make the size more
-# managable. Set this to 0 for no limit. Note that the threshold may be
+# manageable. Set this to 0 for no limit. Note that the threshold may be
 # exceeded by 50% before the limit is enforced.
 
 UML_LIMIT_NUM_FIELDS   = 10

labs/lab1_qmc_statistics/fulltree.sh

@@ -3,7 +3,7 @@
 # Script that displays a recursive formatted folder and file listing
 # @author Corbin
 # @site iamcorbin.net
-#Folder Seperator
+#Folder Separator
 BREAK='-------------------------------------------------------------------------------------'
 
 #Optional: if a folder is passed as an argument, run fulltree on that folder rather than the current folder

manual/afqmc.tex

@@ -181,7 +181,7 @@ \section{Input}
 \begin{itemize}
 \item \textbf{cutoff}. Cutoff applied to Cholesky vectors. Elements of the Cholesky vectors below this value are set to zero.
     Default: 1e-6
-\item \textbf{substractMF}. If ``yes'', apply mean-field substraction based on the ImpSamp trial wave-function. Must set to ``no'' to turn it off.
+\item \textbf{substractMF}. If ``yes'', apply mean-field subtraction based on the ImpSamp trial wave-function. Must set to ``no'' to turn it off.
     Default: yes
 \item \textbf{useCholesky}. If ``yes'', use iterative Cholesky decomposition to factorize 2-electron integral matrix. If ``no'', use eigenvalue decomposition (which is very slow and memory intensive).
     Default: yes

manual/convert4qmc.tex

@@ -316,7 +316,7 @@ \subsubsection{Command line options}
       <basisset name="LCAOBSet">
 \end{shade}
 
-The tag ``cuspCorrection'' in the \texttt{wfj.xml} (or \texttt{wfnoj.xml}) wavefunction file will force correction of the orbitals at the begining of the \qmcpack run. \\
+The tag ``cuspCorrection'' in the \texttt{wfj.xml} (or \texttt{wfnoj.xml}) wavefunction file will force correction of the orbitals at the beginning of the \qmcpack run. \\
 In the ``orbitals`` section of the wavefunction file, a new tag ``cuspInfo'' will be added for orbitals spin-up and orbitals spin-down:
 
 \begin{shade}
@@ -544,13 +544,13 @@ \subsubsection{Supported codes}
 
 
 The main reason to use Quantum Package is to access the CIPSI algorithm to generate a multideterminant wavefunction.
-CIPSI is the prefered choice for generating a selected CI trial wavefunction for \qmcpack.
+CIPSI is the preferred choice for generating a selected CI trial wavefunction for \qmcpack.
 An example on how to use QP for Hartree-Fock and selected CI can be found in Chapter-\ref{sec:cipsi}  of this manual.
 The converter code is actively maintained and co-developed by both \qmcpack and QP developers.
 An HDF5 output file from QP is under development that will mimic the current behavior of the Pyscf output.  
 
 
 \item \textbf{GAMESS}\\
-\qmcpack can use the output of GAMESS\cite{schmidt93} for any type of single determinant calculation (HF or DFT) or multideterminant (MCSCF) calculation. A descripton with an example can be found in the Advanced Molecular Calculations Lab (section-\ref{chap:lab_advanced_molecules}).
+\qmcpack can use the output of GAMESS\cite{schmidt93} for any type of single determinant calculation (HF or DFT) or multideterminant (MCSCF) calculation. A description with an example can be found in the Advanced Molecular Calculations Lab (section-\ref{chap:lab_advanced_molecules}).
 \end{itemize}
 

manual/features.tex

@@ -50,7 +50,7 @@ \subsection{Supported GPU features}
         \item Single Slater determinants with 3D B-spline orbitals. Twist-averaged boundary conditions and complex wavefunctions are fully supported. Gaussian type orbitals are not supported yet.
         \item Hybrid Mixed basis representation in which orbitals are represented as 1D splines times spherical harmonics in spherical regions (muffin tins) around atoms, and 3D B-splines in the interstitial region.
         \item One-body and two-body Jastrows represented as 1D
-          B-splines are supported. Threee-body jastrow functions are
+          B-splines are supported. Three-body jastrow functions are
           not yet supported.
     \end{enumerate}
   \item Semilocal (nonlocal and local) pseudopotentials, Coulomb interaction (electron-electron, electron-ion) and Model periodic Coulomb (MPC) interaction.

manual/gaussian_orbitals_solids.tex

@@ -262,7 +262,7 @@ \section{Generating and using periodic gaussian trial wavefunctions
 from PyscfToQmcpack import savetoqmcpack
 savetoqmcpack(supcell,mf,title=title,kpts=kpts,kmesh=kmesh)
 \end{lstlisting}
-In this call, we simply specify the k-point mesh used in order to force the converter to generate the desired cell. Note that if the parameter \textit{kmesh} is ommited, the converter will still try to ``guess'' it.
+In this call, we simply specify the k-point mesh used in order to force the converter to generate the desired cell. Note that if the parameter \textit{kmesh} is omitted, the converter will still try to ``guess'' it.
 
 
 

manual/hamiltonianobservable.tex

@@ -479,7 +479,7 @@ \section{General estimators}
 
 \subsection{Chiesa-Ceperley-Martin-Holzmann kinetic energy correction}
 
-This estimator calculates a finite size correction to the kinetic energy following the formalism laid out in Ref. \cite{Chiesa2006}.  The total energy can be corrected for finite size effects by using this estimator in conjuction with the MPC correction.
+This estimator calculates a finite size correction to the kinetic energy following the formalism laid out in Ref. \cite{Chiesa2006}.  The total energy can be corrected for finite size effects by using this estimator in conjunction with the MPC correction.
 
 \FloatBarrier
 \begin{table}[h]
@@ -844,7 +844,7 @@ \subsection{Energy density estimator}
               + \sum_{i\ell}\frac{\delta(r-r_i)+\delta(r-\tilde{r}_\ell)}{2}\hat{v}^{eI}(r_i,\tilde{r}_\ell) \nonumber\\ 
     &\qquad   + \sum_{\ell< m}\frac{\delta(r-\tilde{r}_\ell)+\delta(r-\tilde{r}_m)}{2}\hat{v}^{II}(\tilde{r}_\ell,\tilde{r}_m).\nonumber
 \end{align}
-Here $r_i$ and $\tilde{r}_\ell$ represent electon and ion positions, respectively, $\hat{p}_i$ is a single electron momentum operator, and $\hat{v}^{ee}(r_i,r_j)$, $\hat{v}^{eI}(r_i,\tilde{r}_\ell)$, $\hat{v}^{II}(\tilde{r}_\ell,\tilde{r}_m)$ are the electron-electron, electron-ion, and ion-ion pair potential operators (including non-local pseudopotentials, if present).  This form of the energy density is size consistent, \textit{i.e.} the partially integrated energy density operators of well separated atoms gives the isolated Hamiltonians of the respective atoms.  For periodic systems with twist averaged boundary conditions, the energy density is formally correct only for either a set of supercell k-points that correspond to real valued wavefunctions, or a k-point set that has inversion symmetry around a k-point having a real valued wavefunction.  For more information about the energy density, see Ref. \cite{Krogel2013}.
+Here $r_i$ and $\tilde{r}_\ell$ represent election and ion positions, respectively, $\hat{p}_i$ is a single electron momentum operator, and $\hat{v}^{ee}(r_i,r_j)$, $\hat{v}^{eI}(r_i,\tilde{r}_\ell)$, $\hat{v}^{II}(\tilde{r}_\ell,\tilde{r}_m)$ are the electron-electron, electron-ion, and ion-ion pair potential operators (including non-local pseudopotentials, if present).  This form of the energy density is size consistent, \textit{i.e.} the partially integrated energy density operators of well separated atoms gives the isolated Hamiltonians of the respective atoms.  For periodic systems with twist averaged boundary conditions, the energy density is formally correct only for either a set of supercell k-points that correspond to real valued wavefunctions, or a k-point set that has inversion symmetry around a k-point having a real valued wavefunction.  For more information about the energy density, see Ref. \cite{Krogel2013}.
 
 In \qmcpack, the energy density can be accumulated on piecewise uniform three dimensional grids in generalized cartesian, cylindrical, or spherical coordinates.  The energy density integrated within Voronoi volumes centered on ion positions is also available.  The total particle number density is also accumulated on the same grids by the energy density estimator for convenience so that related quantities, such as the regional energy per particle, can be computed easily.
 

manual/integrals_for_afqmc.tex

@@ -1,7 +1,7 @@
 \section{Using PySCF to generate integrals for AFQMC}
 \label{sec:pyscf}
 
-PySCF (https://github.com/sunqm/pyscf) is a collection of electronic structure programs powered by Python. It is the recommended program for the generation of input for AFQMC calculations in QMCPACK. We refer the reader to the documentaion of the code (http://sunqm.github.io/pyscf/) for a detailed description of the features and the functionality of the code. While the notes below are not meant to replace a detailed study of the PySCF documentation, these notes describe useful knowledge and tips in the use of pyscf for the generation of input for QMCPACK. 
+PySCF (https://github.com/sunqm/pyscf) is a collection of electronic structure programs powered by Python. It is the recommended program for the generation of input for AFQMC calculations in QMCPACK. We refer the reader to the documentation of the code (http://sunqm.github.io/pyscf/) for a detailed description of the features and the functionality of the code. While the notes below are not meant to replace a detailed study of the PySCF documentation, these notes describe useful knowledge and tips in the use of pyscf for the generation of input for QMCPACK. 
 
 For molecular systems or periodic calculations at the Gamma point, PySCF provides a routine that generates the integral file in Molpro's FCIDUMP format, which contains all the information needed to run AFQMC with a single determinant trial wave-function. Below is an example using this routine to generate the FCIDUMP file for an 8-atom unit cell of carbon in the diamond structure with HF orbitals. For a detailed description, see PySCF's documentation.  
 \begin{lstlisting}[caption=Simple example showing how to generate FCIDUMP files with PySCF]
@@ -71,7 +71,7 @@ \section{Using PySCF to generate integrals for AFQMC}
 %C 0.8917 2.6751 2.6751'''
 %cell.basis = 'gth-szv'
 %cell.pseudo = 'gth-pade'
-%cell.gs = [10]*3 # 10 grids on postive x direction, => 21^3 grids in total
+%cell.gs = [10]*3 # 10 grids on positive x direction, => 21^3 grids in total
 %cell.verbose = 4
 %cell.build()
 %